On 03/17/2011 04:00 PM, Dario Strbenac wrote:
Can anyone see what's going wrong here ? From the documentation, it should
work. Oh, and importantly, it only has an error if I have the ChIPpeakAnno
package loaded. In a fresh session without ChIPpeakAnno loaded, it works as I
expect.
library(GenomicRanges)
Pks<- GRanges("chr1", IRanges(c(500, 600), width = 100))
elementMetadata(Pks)<- DataFrame(ordID = 1:length(Pks))
I get :
Error in x[[name, exact = FALSE]] :
missing '[[' method for Sequence class GRanges
Hi Dario --
I think the error occurs with
library(GenomicRanges); library(ChIPpeakAnno)
and then your commands, and the workaround is to load ChIPpeakAnno first
library(ChIPpeakAnno)
I think also this specific issue has been addressed in the development
branch (or at least it's not reproducible in this way).
Also, your packages below are a bit of mish-mash; check out
source('http://bioconductor.org/biocLite.R')
old.packages(repos=biocinstallRepos())
and then maybe
update.packages(repos=biocinstallRepos())
Martin
sessionInfo()
R version 2.12.2 (2011-02-25)
Platform: x86_64-pc-mingw32/x64 (64-bit)
locale:
[1] LC_COLLATE=English_Australia.1252
[2] LC_CTYPE=English_Australia.1252
[3] LC_MONETARY=English_Australia.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_Australia.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods
[7] base
other attached packages:
[1] ChIPpeakAnno_1.6.0
[2] limma_3.4.5
[3] org.Hs.eg.db_2.4.1
[4] GO.db_2.4.1
[5] RSQLite_0.9-0
[6] DBI_0.2-5
[7] AnnotationDbi_1.12.0
[8] BSgenome.Ecoli.NCBI.20080805_1.3.16
[9] BSgenome_1.18.0
[10] Biostrings_2.18.0
[11] multtest_2.4.0
[12] Biobase_2.8.0
[13] biomaRt_2.4.0
[14] GenomicRanges_1.2.3
[15] IRanges_1.8.9
loaded via a namespace (and not attached):
[1] MASS_7.3-11 RCurl_1.3-1 splines_2.12.2 survival_2.36-5
[5] tools_2.12.2 XML_2.8-1
--------------------------------------
Dario Strbenac
Research Assistant
Cancer Epigenetics
Garvan Institute of Medical Research
Darlinghurst NSW 2010
Australia
_______________________________________________
Bioc-sig-sequencing mailing list
Bioc-sig-sequencing@r-project.org
https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
--
Computational Biology
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109
Location: M1-B861
Telephone: 206 667-2793
_______________________________________________
Bioc-sig-sequencing mailing list
Bioc-sig-sequencing@r-project.org
https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
